tbuckley/cabot-search huggingface dataset:
Abstract 1170: Scalable co-sequencing of RNA and DNA from individual nuclei
Authors: Timothy R. Olsen, Pranay Talla, Julia Furnari, Shan Zha, Peter Canoll, Jeffrey Bruce, Peter Sims
Journal: Cancer Research (2023)

Abstract A scalable co-assay for single cell mRNA and gDNA sequencing could potentially harmonize the identification of rare cell populations and cell states with corresponding cell-lineage relationships, drug sensitivities, and genetic mutations. Such an assay would provide new insights into the relationship between genetic alterations and tumor cell phenotype. However, simultaneously measuring the genomic and transcriptomic content of individual cells at high throughput remains challenging. Here we present single-cell lithium assisted nucleosome depleted sequencing (scLAND-seq), a scalable method for co-sequencing RNA and DNA from single nuclei that uses the widely available 10x Genomics microfluidics platform. In scLAND-seq, nuclei are treated with a mild detergent, lithium diiodosalicylate, which denatures protein and renders gDNA free of nucleosome packing while preserving the nuclear membrane. The nuclei are then tagmented with Tn5 transposase, which randomly fragments gDNA and integrates universal sequencing adapters. Tagmented nuclei are loaded into a microfluidic droplet generator which co-encapsulates nuclei with beads containing barcoded primers for reverse transcription of mRNA and replication of gDNA. Ultimately two libraries are created: one for nuclear mRNA and one for gDNA. Each library contains barcodes linking it to its nuclei of origin, thus allowing simultaneous analysis of the transcriptome and genome of each nucleus. Once nuclei have been depleted of nucleosomes, all steps can be performed using a 10x Genomics Chromium Controller and 10x Multiome Kit without further experimental modification. We characterize LAND-seq with BJ fibroblasts, a human diploid cell line, and demonstrate the detection of rare subpopulations with copy number variants (CNVs) associated with specific transcriptional clusters. Analysis of transcription start site enrichment indicates near-complete disruption of chromatin structure, resulting in high-complexity libraries that could not be sequenced to saturation even with &amp;gt;1M reads/cell. The corresponding gene expression library is of high-quality, containing ~20,000 gene counts per nuclei. Finally, to demonstrate scLAND-seq’s compatibility with primary cells, we applied scLAND-seq to cryopreserved, human glioblastoma (GBM) surgical specimens, enabling direct investigation into the relationship between phenotype and genotype in thousands of individual cells. Character limit: 2,600 Citation Format: Timothy R. Olsen, Pranay Talla, Julia Furnari, Shan Zha, Peter Canoll, Jeffrey Bruce, Peter Sims. Scalable co-sequencing of RNA and DNA from individual nuclei [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1170.
Abstract 1571: The feasibility and pharmacological mechanism of cucurbitacin E for the treatment of EGFR-TKI-primary resistant NSCLC
Authors: Chun-Han Chen
Journal: Cancer Research (2023)

Abstract Lung cancer ranks the leading cause of cancer death, with an estimated 1.8 million deaths according to the latest global cancer statistics. In the United States, there will be an estimated 236,740 new cases diagnosed, and 130,180 people will die from lung cancer in 2022. In non-small-cell lung cancer (NSCLC) patients, targeted therapies are available for patients with EGFR exon 19 deletion and L858R mutations. However, tumors harboring wild-type EGFR or Kras mutation are not eligible for targeted therapies. Therefore, the development of new drugs to treat primary resistant NSCLC remains urgent needs. Cucurbitacin E (CuE) is a tetracyclic triterpenoid compound extracted from the family of Cucurbitaceae. The data showed that CuE exhibits a significant antiproliferative effect with a GI50 value of 0.03±0.01 μM. Cell cycle analysis revealed that CuE induces G2/M arrest and down-regulates cell cycle regulatory proteins in A549 cells. CuE treatment further increased the expression of cleaved caspase-3/8/9/PARP, and altered the expression of DNA-damaged-related biomarkers. Meanwhile, protein levels of LC3BII and p62, and ROS production were upregulated by CuE. Pharmacological Inhibition of ATM reversed the effects of CuE on autophagy-related proteins. In summary, CuE is a potential drug for the treatment of primary resistant NSCLC. Citation Format: Chun-Han Chen. The feasibility and pharmacological mechanism of cucurbitacin E for the treatment of EGFR-TKI-primary resistant NSCLC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1571.
Abstract 853: The impact of normal tissue density on tumor growth and evolution in a 3D whole-tumor model of lung cancer
Authors: Rafael Ramon Bravo, Mark Robertson-Tessi, Alexander R. Anderson, Robert Gatenby, Scott Antonia, Jhanelle Gray, Amer Beg, Matthew Schabath
Journal: Cancer Research (2023)

Abstract We developed a novel modeling paradigm to specifically recapitulate 3D tissue at the resolution of CT imaging and yet capture single cell information: the population-based model (PBM). This PBM method allowed us to seed a model with individual cells that operate at the CT scale of cubic millimeters and grow to the scale of 10 cubic centimeters or more. We used our PBM to investigate how well-known tumor traits of increased resource consumption and angiogenesis maybe differentially selected by a growing tumor in different densities of normal tissue. We found that tumor phenotypes that reduced consumption and increased angiogenesis grew the fastest in low density normal tissue, and vice versa in high density normal tissue. We ran parameter sweeps of this model using temporal patient data from the NLST dataset, which consisted of untreated tumors in the low-density lung periphery. We saw that specific movement rate and proliferation rate parameters were required to fit the growth speed of the tumors, while a low consumption and high angiogenic phenotype was required to fit the radial density distribution of the tumors. Citation Format: Rafael Ramon Bravo, Mark Robertson-Tessi, Alexander R. Anderson, Robert Gatenby, Scott Antonia, Jhanelle Gray, Amer Beg, Matthew Schabath. The impact of normal tissue density on tumor growth and evolution in a 3D whole-tumor model of lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 853.
Abstract 1570: Novel Myc-dependent compound DL78 selectively induces mitotic catastrophe and cell death in high grade serous ovarian cancer
Authors: Jessica Teitel, Michele Cusato, Margaret Farah, Agharnan Gandhi, Pil Lee, Andrew White, John Takyi-Williams, Bo Wen, Andre Monterio Da Rocha, Analisa DiFeo
Journal: Cancer Research (2023)

Abstract While the rates of new cases and deaths for high grade serous ovarian cancer (HGSC) have declined steadily in the past decade, HGSC remains the fifth leading cause of cancer death in women. As many patients succumb to chemoresistance, there is a need to uncover novel targeted drugs. One way to do so is by drug repurposing. A computational screen, DrugPredict, led to the discovery that amiodarone, an antiarrhythmic, is a potent apoptosis-inducer and Myc-degrader in numerous patient-derived ovarian cancer cell lines. In search of a more selective, but less toxic compound, structure-activity relationship was applied to identify DL78. Due to its structural differences, DL78 is considered to be independent of amiodarone. DL78 lacks hERG activity, retains Myc regulation, and gains selective anticancer properties. This compound produces significant cell death selectively in patient-derived HGSC cells, including isogenic cisplatin-resistant lines, but does not harm non-transformed fallopian tube cells. Cancer cells treated with DL78 arrest prior to anaphase and showcase microtubule abnormalities and upregulation of mitotic regulators. The prolonged arrest leads to loss of Myc, mitotic catastrophe, and apoptosis selectively in the HGSC cells, while fallopian tube cells can cycle normally. DL78’s activity is confirmed to be dependent on Myc expression because targeted inhibition of Myc decreases its potency and prevents the DL78-induced cell cycle arrest. Finally, pharmacokinetic analysis shows that DL78 saturates the tumor following intraperitoneal injection, yet drug concentrations in the blood and liver present at normal levels. Overall, these phenotypes do not show with amiodarone treatment, suggesting that structurally different DL78 performs through a different mechanism. Further classification of this tumor-selective compound may reveal targeted ovarian cancer vulnerabilities. Citation Format: Jessica Teitel, Michele Cusato, Margaret Farah, Agharnan Gandhi, Pil Lee, Andrew White, John Takyi-Williams, Bo Wen, Andre Monterio Da Rocha, Analisa DiFeo. Novel Myc-dependent compound DL78 selectively induces mitotic catastrophe and cell death in high grade serous ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1570.
Abstract 1345: p21 (WAF1/CIP1) drives a secretory phenotype in senescent fibroblasts and promotes bystander cancer cell growth in the tumor microenvironment
Authors: Shengliang Zhang, Kelsey E. Huntington, Lanlan Zhou, Wafik S. El-Deiry
Journal: Cancer Research (2023)

Abstract Cancer associated fibroblasts (CAF) are major stromal cells in the tumor microenvironment (TME) and support cancer cell growth. Chemotherapy can induce CAF senescence in which p21 (the cyclin-dependent kinase inhibitor) permanently arrests the cell cycle. Cellular senescence and its associated secretory phenotype (SASP) can promote cancer progression and lead to drug resistance. We explored molecular mechanisms of p21 in the cellular communication between cancer and senescent fibroblasts. We induced fibroblast cell senescence by treatment with etoposide. Cellular senescence was confirmed by cytokine profiling, beta-gal staining and high p21 expression. To evaluate the role of p21 in the SASP of senescent fibroblasts, we transiently knocked down p21 expression in senescent fibroblast cells using siRNA. SA-beta-gal staining showed a strong beta-gal expression around nuclei in the senescent fibroblast cells with the knockdown of p21, which is the same as it was in the cells with siRNA control. Further cytokine profiling showed two panels of SASP upon p21 knockdown in senescent cells: 1) decrease of cytokines such as CCL2 and IL8 and 2) increase of cytokines such TNF-alpha correlated to the knockdown of p21 in the senescent cells. These results suggest that p21 drives a SASP in senescent fibroblast cells, in addition to its function in cell cycle arrest. We examined the effect of the p21-driven SASP in senescent fibroblasts on bystander cancer cell growth in the TME. Our co-culture system showed knockdown of p21 in senescent fibroblasts suppressed bystander cancer cell growth. We found that knockdown of TNF partially blocked the antiproliferation effect of p21-knockdown on bystander cancer cells. Our results suggest that senescent fibroblasts support bystander cancer cell growth via a p21-driven SASP in the TME and provides a new strategy for targeting p21-driven SASP in the TME for cancer therapy. Citation Format: Shengliang Zhang, Kelsey E. Huntington, Lanlan Zhou, Wafik S. El-Deiry. p21 (WAF1/CIP1) drives a secretory phenotype in senescent fibroblasts and promotes bystander cancer cell growth in the tumor microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1345.
Abstract 1869: Preclinical evaluation of mosunetuzumab for the treatment of relapsed/refractory chronic lymphocytic leukemia
Authors: Kathy Barrett, Kai Lu, Hyun Yong Jin, Rosie Millen, Marcus Lefebure, Yanwen Jiang
Journal: Cancer Research (2023)

Abstract Background: CD20 x CD3 T-cell engaging bispecific antibodies, such as Mosunetuzumab (Mosun), have shown promising efficacy in Non-Hodgkin’s lymphoma. However, their role in treating chronic lymphocytic leukemia (CLL) is still uncertain. CLL, a clonal disease of mature B cells, is associated with high B/T cell ratios and diminished T cell activation and function, including the inability to form strong immunosynapses (Ramsay et al, J Clinical Investigation, 2008). Herein, we explore whether Mosun could overcome these barriers and elicit strong T-cell mediated B-cell killing in CLL samples. Methods: PBMCs from CLL patients and healthy donors were exposed to a titration of Mosun for 48 and 72 hours and analyzed for B cell death with flow cytometry. Markers of T cell activation and exhaustion were quantified in CD4 and CD8T cells and within their CD45RA/CCR7 subsets. The concentrations of secreted cytokines were measured by ELISA. To study the impact of high B/T ratio on B cell killing, B cells were isolated from healthy donor PBMC and added back to autologous PBMC to attain B/T ratios seen in CLL patient samples. Results: After 48 hours with 0.04ug/ml Mosun, the percentage of dead B cells in healthy-donor samples (n=9) exceeded that in CLL samples (n=7) by four-fold (54.2 + 17.9 vs: 12.9 + 17.5%, p=0.0004). Under the same conditions, significantly more T cells expressed activation markers in healthy donors than in CLL patients, with 58.8 +17.1% of healthy donor CD8T cells expressing both CD69 and CD25 compared to and 31.4 +21.4% of CLL CD8T cells (p=0.013). The mean concentration of Granzyme B secreted by healthy donor samples upon Mosun treatment was over ten times higher than by CLL patient samples. Reconstitution of a healthy donor sample to a B/T ratio of 10 resulted in decreased B cell killing (29.7% dead B cells vs: 70.5% in un-reconstituted) without affecting T cell activation (62.9% CD69+CD25+ CD8T cells versus 56.2% in un-reconstituted). Conclusions: Although single-agent Mosun treatment can activate T-cells in CLL patient samples and result in B-cell death, the response is suboptimal due to a number of factors, including deficient T cell activation and high B/T ratio. Ongoing work is focusing on evaluating drug partners to debulk CLL B cells or prime CLL T cells for better B-cell killing by Mosun. Citation Format: Kathy Barrett, Kai Lu, Hyun Yong Jin, Rosie Millen, Marcus Lefebure, Yanwen Jiang. Preclinical evaluation of mosunetuzumab for the treatment of relapsed/refractory chronic lymphocytic leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1869.
Abstract 1347: PAUF stimulates monocytes and induces their differentiation into tumor-associated macrophages
Authors: Fen Jiang, Yeon Jeong Kim, Yun Yong Park, Tae Heung Kang, Sang Seok Koh
Journal: Cancer Research (2023)

Abstract Background: One of the main reasons for the failure of cancer treatments is that the biological function of therapeutic target molecules is only studied in cancer cells. Therefore, the dynamic and complex interactions between cancer and stromal cells in the tumor microenvironment (TME) should be investigated. TME-specific stromal cells include various cells, with tumor-associated macrophages (TAMs) being one of the major players. TAM are differentiated from monocytes, as immature monocytes recognize molecules derived from infected cells or foreign substances, become activated, and may differentiate into anti-tumoral M1 macrophages or pro-tumoral M2 macrophages (called TAMs). TAMs induce immune evasion of cancer cells in the TME, leading to active proliferation and metastasis of cancer cells. The presence of TAMs in the TME is associated with poor prognosis in various cancers. PAUF is a protein that is secreted by cancer cells, and it exerts tumor-promoting effects through autocrine and paracrine mechanisms. Compared to the autocrine actions, the paracrine effects of PAUF on immune cells in the TME are less understood. Objective: This study aimed to evaluate 1) the role of PAUF as a TME modulator, and specifically, a TAM inducer and 2) the potentiality of PAUF antibody as a blocker of TAM transformation. Methods and Results: In a monocyte-PAUF co-culture system, PAUF (tested at two concentrations, 0.1 and 0.5 μg/mL) demonstrated strong chemoattractant effects on monocytes (~400% of that caused by PBS), which were blocked by TLR2/4 inhibitors. PAUF also induced differentiation of monocytes into macrophages, which were identified to be TAM, using flow cytometric analysis and ELISA method. Moreover, these PAUF-induced TAM demonstrated T cell suppressing capacities. Finally, in a CFPAC-1 human cancer orthotopic mouse model, a humanized monoclonal PAUF-antibody diminished 60-70% of infiltrated TAM (p&amp;lt;0.01), quantified using an immunofluorescence assay (IFA). Conclusion: In conclusion, this study provides direct evidence that PAUF can differentiate monocytes into TAM of immune-suppressing functions, and the PAUF neutralization-induced TAM infiltration blocking suggests potential combination use of PAUF antibody with immunotherapeutics for cancer treatments. Citation Format: Fen Jiang, Yeon Jeong Kim, Yun Yong Park, Tae Heung Kang, Sang Seok Koh. PAUF stimulates monocytes and induces their differentiation into tumor-associated macrophages [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1347.
Abstract 795: T-cell mediated response to emerging COVID-19 strains in patients with cancer studied via deep learning
Authors: Olga Lyudovyk, Yuval Elhanati, Artem Streltsov, Quaid Morris, Santosha Vardhana, Benjamin Greenbaum
Journal: Cancer Research (2023)

Abstract Cancer patients, particularly those receiving B cell-depleting therapy for lymphoid malignancies, are at risk of prolonged SARS-CoV-2 infection, poorer clinical outcomes, and delayed initiation or disruption of cancer-directed therapy (Lee at al., 2022, Clark et al., 2021). We first studied T-cell mediated response to the Wuhan strain of SARS-CoV-2 in a cohort of 69 patients with hematologic and solid cancers, including 18 patients who received prior B-cell depleting therapy. Patients with prolonged COVID-19 clearance, defined by a positive PCR test for longer than 30 days, had a broad but poorly converged CD8+ dominant response and a lacking CD4+ response. To conduct this analysis, we performed bulk T-cell receptor (TCR) sequencing of 121 blood samples and tracked over time TCR repertoire statistics such as clonality, convergence, breadth, and depth of COVID-19-associated TCRs during the active and convalescent periods of COVID-19 infection. These SARS-CoV-2-associated TCRs were identified leveraging immunoSEQ T-MAP database (Snyder et al., 2020), a set of TCR sequences derived from COVID-19 patients and experimentally identified as responsive to MHC Class I and II epitopes from the Wuhan SARS-CoV-2 strain using the multiplex identification of TCR antigen assay (Klinger et al., 2015). To extend our TCR repertoire analysis to other SARS-CoV-2 variants, including Omicron, we developed a deep learning (DL) method to predict TCR specificities for new SARS-CoV-2 epitopes. This DL approach also permits the identification of SARS-CoV2-responsive TCRs private to an individual. Combining this DL approach with our TCR statistics methodology, we studied the dynamics of T-cell response to COVID-19 vaccinations in a cohort of 50 patients with cancer and analyzed TCR repertoire characteristics associated with different degrees of COVID-19 severity in a cohort of 42 cancer patients who contracted the Omicron. Understanding cellular response to novel infections is critical for patient care in the context of cancer, and our novel DL-based approach can leverage existing datasets to analyze and track response to emerging viral strains. Citation Format: Olga Lyudovyk, Yuval Elhanati, Artem Streltsov, Quaid Morris, Santosha Vardhana, Benjamin Greenbaum. T-cell mediated response to emerging COVID-19 strains in patients with cancer studied via deep learning [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 795.